Detective Constable Jayne Bretherton today revealed two fishing nets believed to have come from the stricken vessel had been found by searchers along the same stretch of coastline.
It was also hoped the dive squad would reach the spot where the vessel went down.
"The boat is believed to have lost power, so an assessment will be made to determine how that may have happened," said Bretherton.
There would be no ground crews out today, she said.
West Coast police said yesterday there was still a good chance the pair could be found alive, Senior Sergeant Paul Watson of Greymouth said.
Search teams were waiting for a break in the weather, which had been hampering efforts to search the shoreline.
"The indications are there is still quite a high chance of survivability, if they had been able to get out of the water," Watson said.
Although the liferaft had been found inflated, there was no indication the two missing fisherman had managed to use it.
About a dozen police and volunteers were ready to continue searching the shoreline today, weather permitting.
Haast-based commercial helicopters had also been pressed into service.
They also relied on having suitable volunteers to search the rugged coast.
"A lot of the time they're hampered by what they can do given the ruggedness of the shoreline," Watson said.
The Wendy J got into trouble while trying to shelter from a vicious storm on Thursday night.
Brown said he knew something was wrong when someone spotted a liferaft but no wreckage.
The Greymouth-based fishing company had two boats in the Jackson Bay area at the time, the Te Aroha and the Wendy J.
"I got hold of the skipper on the Te Aroha and asked if they were alright. Sometimes you don't hear from a boat for a day. The boat had been in contact with the Wendy J the night before and they were looking to anchor up at Smoothwater Bay."
He contacted Maritime Rescue Control and they immediately sent a helicopter to search the coastline south of Jackson Bay.
Thomas was rescued from the shoreline and taken to the nearest settlement, at Neils Beach, from where he rang Brown, who then drove from Greymouth to pick him up.
"Mark was worried about his crew," Brown said.
"He suspected a craypot rope got wrapped around the propeller and stalled the engine. The boat started foundering in the heavy seas and there was chaos on the boat as they scrambled for lifejackets.
"Mark was thrown into the water and somehow grabbed hold of a life ring in the water."
Brown said he believed his skipper was lucky to have survived, but his strong will had played an important role.
"He was just wearing shorts and a T-shirt and was in the water a long time. He sheltered in a flax bush on land and drank water from a creek.
"He was cut and scratched, very tired and cold when I picked him up. His foot was cut and bandaged and he was sore and struggled to walk."
He was taken to Grey Base Hospital and discharged, but yesterday was readmitted because of an infection.
Thomas had just installed a new diesel engine to his boat, which he fishes under contract to Westfleet.
"We feel for the families of the missing crew and just hope by chance they are alright,"
Brown said.
Okuru-based police marine search and rescue adviser and long-time local fisherman Kerry Eggeling said narrow and rocky Smoothwater Bay was "notorious" for big seas.
"In the past 10 to 15 years there's been two or three reasonably major incidents there, and a whole swag of near-misses."
Weather conditions on Thursday night and Friday morning had been "horrendous" with wind gusts of about 80km/h on land.
The boat made no distress call and did not set off its emergency locator beacon.
The Rescue Co-ordination Centre said the first notification it received was from the aircraft that spotted the liferaft.
Max Dowell, who runs the marine radio out of Hokitika, said that up until 10 years ago fishermen would check in with him morning and night, but they "fell out of the habit" after the radio service transferred to Greymouth.
"Twenty-odd years ago, 40 boats would call in morning and night, particularly in the tuna season."
Now, just five Greymouth boats called in regularly.
- Greymouth Star